The complex repeats of Dictyostelium discoideum

In the course of determining the sequence of the Dictyostelium discoideum g enome we have characterized in detail the quantity and nature of interspers ed repetitive elements present in this species. Several of the most abundan t small complex repeats and transposons (DIRS-1; TRE3-A,B; TRE5-A; skipper; Tdd-4; H3R) have been described previously. In our analysis we have identi fied additional elements. Thus, we can now present a complete list of compl ex repetitive elements in D. discoideum. All elements add up to 10% of the genome. Some of the newly described elements belong to established classes (TRE3-C, D; TRE5-B,C; DGLT-A,P; Tdd-5). However, we have also defined two n ew classes of DNA transposable elements (DDT and thug) that have not been d escribed thus far. Based on the nucleotide amount, we calculated the least copy number in each family. These vary between <10 up to >200 copies. Uniqu e sequences adjacent to the element ends and truncation points in elements gave a measure for the fragmentation of the elements. Furthermore, we descr ibe the diversity of single elements with regard to polymorphisms and conse rved structures. All elements show insertion preference into loci in which other elements of the same family reside. The analysis of the complex repea ts is a valuable data resource for the ongoing assembly of whole D. discoid eum chromosomes.